Contacts of the helix formed by residues 376 - 391 (chain A) in PDB entry 5WWZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A GLY 3.9 5.4 - - - +
326A GLN* 4.6 3.1 - - - +
375A GLY* 1.3 72.4 - - - +
377A PRO* 1.3 65.7 - - + +
378A GLU* 4.5 3.4 - - + +
379A ASN* 3.0 32.4 + - - +
380A VAL* 2.7 32.7 + - - +
389B MET 4.4 11.1 + - - +
390B HIS* 6.2 0.2 - - - -
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Residues in contact with PRO 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A GLY 3.1 20.2 - - - +
327A THR* 4.1 22.7 - - + -
375A GLY 3.6 1.5 - - - +
376A MET* 1.3 84.8 - - + +
378A GLU* 1.3 62.0 + - - +
380A VAL* 3.9 1.1 - - + +
381A ASP* 3.1 33.8 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A MET* 3.3 3.2 - - + +
377A PRO* 1.3 79.0 - - - +
379A ASN* 1.3 65.3 + - - +
381A ASP* 3.7 6.5 + - - +
382A ARG* 3.3 21.0 + - - +
392B ALA* 6.3 3.1 - - + -
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Residues in contact with ASN 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A THR* 3.1 26.1 + - - +
357A HIS 4.2 2.2 + - - -
358A THR* 3.5 15.9 - - + +
376A MET* 3.0 28.7 + - + +
378A GLU* 1.3 81.0 - - - +
380A VAL* 1.3 58.1 + - - +
382A ARG* 3.3 6.6 + - - +
383A ALA* 2.9 23.0 + - - +
389B MET 3.9 7.3 + - - -
391B ILE 2.9 27.0 + - - -
392B ALA* 3.9 4.4 - - - +
393B MET* 3.2 29.8 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 3.9 13.0 - - + +
329A VAL* 3.5 41.1 - - + -
358A THR* 4.2 4.9 - - + -
373A VAL* 4.0 15.8 - - + +
374A THR 3.8 6.1 - - - -
375A GLY* 3.4 33.7 - - - +
376A MET 2.7 23.9 + - - +
377A PRO 3.9 4.3 - - - +
379A ASN* 1.3 70.6 - - - +
381A ASP* 1.3 65.2 + - - +
383A ALA* 3.2 2.3 + - - +
384A ARG* 2.8 27.8 + - - +
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 5.7 2.9 - - - +
377A PRO* 3.1 22.6 + - - +
378A GLU* 4.1 6.0 - - - +
380A VAL* 1.3 81.5 - - - +
382A ARG* 1.3 56.8 + - - +
384A ARG* 3.4 16.4 + - - +
385A GLU* 3.0 29.3 + - - +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A THR* 4.0 3.1 - - + -
378A GLU 3.3 13.2 + - - +
379A ASN* 3.5 9.9 - - - +
380A VAL 3.2 0.4 - - - -
381A ASP* 1.3 79.3 - - - +
383A ALA* 1.3 57.3 + - - +
385A GLU* 3.3 11.2 + - - +
386A GLU* 2.9 32.7 + - + +
393B MET* 4.0 29.2 - - + -
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ILE* 4.3 1.4 - - + +
356A THR* 3.5 25.1 - - - +
358A THR* 3.7 3.6 - - - +
360A ILE* 4.3 8.3 - - + -
373A VAL* 3.6 23.6 - - + -
379A ASN 2.9 17.3 + - - +
380A VAL 3.2 5.1 + - - +
382A ARG* 1.3 74.8 - - - +
384A ARG* 1.3 63.3 + - - +
386A GLU* 3.3 4.1 + - - +
387A ILE* 3.0 30.7 + - - +
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A VAL* 3.4 27.8 - - + +
330A GLN 2.7 29.7 + - - +
331A VAL* 3.8 31.0 - - + +
332A ARG 5.2 1.0 - - - +
373A VAL* 5.2 0.4 - - - +
380A VAL 2.8 16.1 + - - +
381A ASP* 3.7 17.3 + - - +
383A ALA* 1.3 76.5 - - - +
385A GLU* 1.3 63.0 + - - +
387A ILE* 3.4 2.6 + - - +
388A GLU* 3.0 52.2 + - - +
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Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ASP 3.0 17.6 + - - +
382A ARG* 3.5 10.1 - - - +
384A ARG* 1.3 75.2 - - - +
386A GLU* 1.3 59.2 + - + +
388A GLU* 3.3 7.9 + - - +
389A MET* 2.9 36.5 + - + +
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 3.9 24.5 - - + +
355A GLN* 4.5 9.7 - - - +
356A THR* 4.0 16.6 - - + +
382A ARG* 2.9 21.2 + - + +
383A ALA 3.3 5.8 + - - +
385A GLU* 1.3 76.5 - - + +
387A ILE* 1.3 57.9 + - - +
389A MET* 3.3 29.3 + - - +
390A HIS* 2.6 36.7 + - - -
393B MET* 4.3 17.5 - - + +
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A VAL* 3.8 22.9 - - + -
333A VAL* 3.9 18.8 - - + -
341A VAL* 3.8 29.2 - - + +
349A ILE* 4.5 4.5 - - + -
352A ILE* 4.3 13.5 - - + -
360A ILE* 4.5 9.9 - - + -
371A PHE* 4.1 22.2 - - + -
373A VAL* 4.1 23.8 - - + -
383A ALA 3.0 17.0 + - - +
384A ARG 3.7 4.5 - - - +
386A GLU* 1.3 77.5 - - - +
388A GLU* 1.3 62.0 + - - +
390A HIS* 3.2 15.4 + - - +
391A ILE 3.7 8.1 + - - +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 4.4 10.9 - - + +
332A ARG 5.6 4.2 - - - +
333A VAL* 5.6 3.4 - - + -
384A ARG* 3.0 53.9 + - - +
385A GLU* 4.0 6.1 - - + +
387A ILE* 1.3 76.8 - - + +
389A MET* 1.3 60.8 + - - +
390A HIS 3.3 0.6 + - - -
391A ILE 3.6 21.1 - - - +
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Residues in contact with MET 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A GLU* 2.9 21.8 + - + +
386A GLU* 3.3 27.8 - - - +
387A ILE 3.2 0.4 - - - -
388A GLU* 1.3 77.6 - - - +
390A HIS* 1.3 77.5 + - + +
391A ILE 3.5 0.2 - - - -
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 4.5 17.2 - - + +
341A VAL* 4.6 12.8 - - + -
348A THR* 3.6 28.2 - - + +
352A ILE* 3.9 22.9 - - + +
386A GLU* 2.6 31.4 + - - -
387A ILE* 3.2 7.2 + - - +
389A MET* 1.3 95.7 - - + +
391A ILE* 1.3 62.2 + - + +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A VAL* 4.5 10.6 - - - +
334A PRO* 4.8 6.6 - - - +
337A VAL* 3.6 45.9 - - + +
340A LEU* 3.9 14.8 - - + -
341A VAL* 5.3 2.5 - - + -
387A ILE 3.7 7.6 + - - +
388A GLU* 3.6 19.3 + - - +
389A MET 3.5 1.0 - - - -
390A HIS* 1.3 84.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il